lsmquant/subworkflows/local/numorph_preprocessing/meta.yml at 9b1e779e46bf16293fdf7ebaca89ef67c68586a4 · CaroAMN/lsmquant · GitHub

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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
name: "numorph_preprocessing"
description: preprocessing (intensity adjustment, alignment, stitching) of 2D single channel single tile TIFF images.
keywords:
  - intensity
  - alignment
  - stitching
  - tiff
components:
  - numorphintensity
  - numorphalign
  - numorphstitch
  - mat2json
input:
  - samplesheet:
      type: tuple
      description: |
        The input channel containing the metadata, image directory and parameter file.
        Structure: [ val(meta), path(img_directory), path(parameter_file)]
      pattern: "*.{tif/tiff/csv}"
output:
  - stitched:
      type: path
      description: |
        Channel containing path to stitched Tiff files
        Structure: [ val(meta), path(stitched) ]
      pattern: "*.tif/tiff"
  - intensity_thresholds:
      type: file
      description: |
        Channel containing intensity threshold (MAT) file
        Structure:  path(thresholds_mat)
      pattern: "*.mat"
  - NM_variables:
      type: file
      description: |
        Channel containing numorph processing parameter file (MAT)
        Structure:  path(NM_variables.mat)
      pattern: "*.mat"
  - versions:
      type: file
      description: |
        File containing software versions
        Structure: [ path(versions.yml) ]
      pattern: "versions.yml"
authors:
  - "@CaroAMN"
maintainers:
  - "@CaroAMN"